| 1. |
- Falster, Daniel, et al.
(författare)
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AusTraits, a curated plant trait database for the Australian flora
- 2021
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Ingår i: Scientific Data. - : Nature Portfolio. - 2052-4463. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- We introduce the AusTraits database - a compilation of values of plant traits for taxa in the Australian flora (hereafter AusTraits). AusTraits synthesises data on 448 traits across 28,640 taxa from field campaigns, published literature, taxonomic monographs, and individual taxon descriptions. Traits vary in scope from physiological measures of performance (e.g. photosynthetic gas exchange, water-use efficiency) to morphological attributes (e.g. leaf area, seed mass, plant height) which link to aspects of ecological variation. AusTraits contains curated and harmonised individual- and species-level measurements coupled to, where available, contextual information on site properties and experimental conditions. This article provides information on version 3.0.2 of AusTraits which contains data for 997,808 trait-by-taxon combinations. We envision AusTraits as an ongoing collaborative initiative for easily archiving and sharing trait data, which also provides a template for other national or regional initiatives globally to fill persistent gaps in trait knowledge.
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| 2. |
- Agirre, Jon, et al.
(författare)
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The CCP4 suite: integrative software for macromolecular crystallography
- 2023
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Ingår i: Acta Crystallographica Section D. - : INT UNION CRYSTALLOGRAPHY. - 2059-7983. ; 79, s. 449-461
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Tidskriftsartikel (refereegranskat)abstract
- The Collaborative Computational Project No. 4 (CCP4) is a UK-led international collective with a mission to develop, test, distribute and promote software for macromolecular crystallography. The CCP4 suite is a multiplatform collection of programs brought together by familiar execution routines, a set of common libraries and graphical interfaces. The CCP4 suite has experienced several considerable changes since its last reference article, involving new infrastructure, original programs and graphical interfaces. This article, which is intended as a general literature citation for the use of the CCP4 software suite in structure determination, will guide the reader through such transformations, offering a general overview of the new features and outlining future developments. As such, it aims to highlight the individual programs that comprise the suite and to provide the latest references to them for perusal by crystallographers around the world.
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| 3. |
- Graversgaard, Morten, et al.
(författare)
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Policies for wetlands implementation in Denmark and Sweden - historical lessons and emerging issues
- 2021
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Ingår i: Land use policy. - : Elsevier. - 0264-8377 .- 1873-5754. ; 101
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Tidskriftsartikel (refereegranskat)abstract
- Natural wetlands used to cover a significant part of the landscape, but these ecosystems have declined by >50% worldwide, and even more in Denmark and Sweden. However, since the 1980s, various policies have been implemented to restore and create wetlands. This study provides a comprehensive historical overview of policies used to stimulate the creation and restoration of wetlands in Denmark and Sweden, and also analyses what factors have facilitated participation or have been barriers for landowners. The analysis of wetlands implementation programmes in Denmark showed a change towards narrower focus on nitrogen reduction from 1998 and onwards, whereas policies in Sweden often have had a wider multifunctional purpose. In both countries, there has been a change in the compensation structure from a lump sum to annual payments, parallel to an observed increase in costs for wetlands implementation. There is still a large potential for recreating many more wetlands, and the national targets have not been reached in neither Denmark nor Sweden. Key success factors, for future wetlands implementation are sufficient compensation levels, flexible scheme designs and information-based strategies documenting relevant benefits and sustainability issues. In general, more advice and support from the state, regional and local participants, and farmers organisations, are required to increase the participation and achieve successful and cost-efficient wetlands implementation. A collaborative and catchment-based approach holds promise, where wetland governance can serve as a platform for collaboration between policy bodies and between farmers. Additionally, politicians and decision makers need to accept the area targets presented to them when setting policy goals for wetlands implementation, and to accept that restoring and constructing wetlands requires long implementation times before results can be demonstrated.
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| 4. |
- Wills, John W., et al.
(författare)
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Image-Based Cell Profiling Enables Quantitative Tissue Microscopy in Gastroenterology
- 2020
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Ingår i: Cytometry Part A. - : WILEY. - 1552-4922 .- 1552-4930. ; 97:12, s. 1222-1237
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Tidskriftsartikel (refereegranskat)abstract
- Immunofluorescence microscopy is an essential tool for tissue-based research, yet data reporting is almost always qualitative. Quantification of images, at the per-cell level, enables "flow cytometry-type" analyses with intact locational data but achieving this is complex. Gastrointestinal tissue, for example, is highly diverse: from mixed-cell epithelial layers through to discrete lymphoid patches. Moreover, different species (e.g., rat, mouse, and humans) and tissue preparations (paraffin/frozen) are all commonly studied. Here, using field-relevant examples, we develop open, user-friendly methodology that can encompass these variables to provide quantitative tissue microscopy for the field. Antibody-independent cell labeling approaches, compatible across preparation types and species, were optimized. Per-cell data were extracted from routine confocal micrographs, with semantic machine learning employed to tackle densely packed lymphoid tissues. Data analysis was achieved by flow cytometry-type analyses alongside visualization and statistical definition of cell locations, interactions and established microenvironments. First, quantification of Escherichia coli passage into human small bowel tissue, following Ussing chamber incubations exemplified objective quantification of rare events in the context of lumen-tissue crosstalk. Second, in rat jejenum, precise histological context revealed distinct populations of intraepithelial lymphocytes between and directly below enterocytes enabling quantification in context of total epithelial cell numbers. Finally, mouse mononuclear phagocyte-T cell interactions, cell expression and significant spatial cell congregations were mapped to shed light on cell-cell communication in lymphoid Peyers patch. Accessible, quantitative tissue microscopy provides a new window-of-insight to diverse questions in gastroenterology. It can also help combat some of the data reproducibility crisis associated with antibody technologies and over-reliance on qualitative microscopy. (c) 2020 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of International Society for Advancement of Cytometry.
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